Absolutely my favorite of those is Re-Volt. Some of the most realistic (sometimes frustratingly so) physics ever in a driving game (of a sort, since you're "driving" RC cars). I still drag that out and play it, and I rarely meet anyone who's even heard of it.

One for the SNES that never made it out of Japan and really should have-- Front Mission. Tremendous mecha/strategy/battle game, only available in English as a rom.

Most of the rest that I can think of right off are more in the line of cult games-- ones that aren't widely known among the general population, but much beloved among gamers-- things like The Neverhood, Grim Fandango or ActRaiser.

Klonoa 2: Lunatea's Veil.
It's a platformer for the PS2 and is the sequel to Klonoa: Door To Phantomile for the PSX.

I thought that the Klonoa series was dumb but now since I saw these lets play I think its pretty good.

A game that nobody has ever heard of that is good is, Pokemon XD: Gale of Darkness if your a pokemon fan its pretty damn good actually and I don't know if you guys know the game Super Mario Sunshine thats really good to.

007: everything or nothing, also Conflict: Desert storm (I own everything or nothing for PS2, rented C:DS multiple times). Both have EPIC co-op. If only PS2 had internets back then.... and now... and people still used it...

Zack & Wiki.
Probably one of the most underrated games ever. Zack & Wiki: Quest for Barbaros' Treasure is a puzzle game for the Wii. The puzzles really make you think outside of the box, the art style is gorgeous, the levels keep introducing interesting quirks to keep you interested, the music is astounding, and the humor is actually pretty funny.
Here's part 1 of a walkthrough.

If you have a Wii, it's a must-buy.

Meteos.
An action-puzzler for the DS, though it's more "action" than "puzzle." The gameplay is fast-paced and addicting, the art style wildly and wonderfully varies from stage to stage, the music is amazingly interactive, and it has a ton of universe content, making for a lot of spin-off opportunities.
Here's some gameplay of Anasaze vs. Megadom.

Beyond Good & Evil
Heck, this game is probably famous for being underrated. The gameplay is awesome, being easy to control and reminds me of Legend of Zelda. the plot is intense, engaging, and movie-quality. The same can be said for the art & music. Extremely well-done. Epic is an understatement. The
Part 1 of a walkthrough: